Daniel:Notebook/Haplotyping/BEAGLE

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Processing BEAGLE Data[edit]

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This page describes the data processing for the BEAGLE data in the haplotyping project. For data locations, visit the Data Map.

  • The BEAGLE manual can be found here

Processing[edit]

  1. BEAGLE requires a starting genotyping file. This file needs to include all genotypes at all the relevant sites. Sites that are known can have a 0|1 or 1|0. Sites that are unknown are a 0/1. For the purposes of this project, I first started with the Hi-C data, but it can be done with any hapcut output file. The first step in the pipeline converts a HAPCUT output file to a vcf with the genotypes assigned for the largest block (given 0|1 or 1|0). The other SNPs are imputed by BEAGLE (assigned 0/1 by the program).
    1. Shell file for looping through protocol and MATLAB file
  2. Next, we run BEAGLE
    1. Shell script for BEAGLE imputations